Understanding biological processes such as cellular communication, immune responses, developmental programs, and tumor microenvironments requires knowledge of both molecular composition and the spatial organization of cells. Traditional microscopy techniques provide high molecular sensitivity through fluorescent probes but can only detect a limited number of biomarkers simultaneously. Conversely, single-cell sequencing can reveal entire transcriptomes, making it a powerful tool for classifying cells into types and states, but it requires tissue dissociation, leading to a loss of crucial spatial information.
This HALRIC pilot project aims to bridge this gap by developing and optimizing multiplex fluorescence in situ hybridization (FISH) methods for spatial transcriptomics. By enabling the detection of multiple mRNA species—potentially up to the whole transcriptome—while preserving subcellular localization through iterative labeling and imaging, this approach provides a more comprehensive understanding of molecular interactions within tissue architecture. Such advancements are critical for the next generation of personalized medicine, where molecular diagnostics and novel biomarkers with prognostic capabilities can guide treatment decisions.
The project is a collaboration between researchers from two countries, involving two advanced imaging core facilities—Lund University Bioimaging Centre (LBIC) in Sweden and the Danish Molecular Biomedical Imaging Center (DaMBIC) at the University of Southern Denmark—along with researchers at Skåne University Hospital. Together, they aim to refine best practices, develop probe libraries, and improve data analysis workflows, ensuring that spatial transcriptomics becomes a widely accessible tool for biomedical research and clinical applications.
By integrating cutting-edge molecular imaging with spatially resolved transcriptomics, this project supports the development of advanced diagnostics and targeted therapies, directly contributing to HALRIC’s mission of fostering cross-border collaboration and accelerating innovation in biomedical imaging.
For further information about this HALRIC pilot project, please contact:
Nils Norlin, Lund University
